Contacts of the helix formed by residues 290 - 308 (chain C) in PDB entry 3SF4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 290 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C TYR* 2.8 31.6 + - + +
288C LEU* 4.4 7.6 - - + +
289C GLN* 1.3 72.5 - - - +
291C TYR* 1.3 55.6 + - - +
292C GLU* 3.5 8.8 + - - +
293C LYS* 3.1 48.2 + - - +
294C ALA* 3.1 22.9 + - - +
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Residues in contact with TYR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C THR* 4.2 32.4 + - + +
289C GLN* 3.8 41.6 + - + +
290C ASP* 1.3 68.6 + - - +
292C GLU* 1.3 60.1 + - - +
294C ALA* 3.5 6.7 - - + +
295C ILE* 2.9 36.7 + - + +
324C ALA* 4.5 15.3 - - + +
327C ALA* 3.8 31.1 - - + +
328C LEU* 3.6 35.7 - - + -
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ASP* 3.2 8.8 + - - +
291C TYR* 1.3 78.4 - - - +
293C LYS* 1.3 62.9 + - + +
295C ILE* 3.4 5.3 + - - +
296C ASP* 3.0 25.6 + - - +
328C LEU* 4.6 9.8 - - + +
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Residues in contact with LYS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LYS* 5.4 3.6 - - - +
285C TYR* 3.7 43.2 + - + +
290C ASP* 3.1 29.0 + - - +
292C GLU* 1.3 78.1 - - + +
294C ALA* 1.3 65.0 + - - +
296C ASP* 3.3 6.8 + - - +
297C TYR* 3.1 34.4 + - + -
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLY* 3.5 27.9 - - - +
285C TYR* 3.7 4.4 - - - +
286C THR* 3.6 17.9 - - - +
290C ASP 3.1 14.1 + - - +
291C TYR* 3.5 16.2 - - + +
292C GLU 3.2 0.2 - - - -
293C LYS* 1.3 78.6 - - - +
295C ILE* 1.3 56.6 + - - +
297C TYR 3.4 0.5 + - - -
298C HIS* 2.9 39.0 + - + -
324C ALA* 5.0 4.3 - - + -
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Residues in contact with ILE 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TYR 2.9 21.0 + - - +
292C GLU* 3.7 5.4 - - - +
294C ALA* 1.3 73.1 - - - +
296C ASP* 1.3 62.2 + - - +
298C HIS* 3.7 5.5 - - - +
299C LEU* 2.8 50.6 + - + +
321C LEU* 4.4 4.0 - - + -
324C ALA* 3.5 26.2 - - + -
325C TYR* 3.6 44.4 - - + +
328C LEU* 3.6 23.6 - - + -
330C ASN* 5.7 0.2 - - - +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C GLU 3.0 14.5 + - - +
293C LYS* 3.5 13.1 - - - +
295C ILE* 1.3 80.1 - - - +
297C TYR* 1.3 70.0 + - - +
299C LEU* 3.4 8.9 + - - +
300C LYS* 3.1 53.3 + - - +
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Residues in contact with TYR 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LYS* 4.2 17.6 - - - +
262C LEU* 3.8 15.5 - - + +
266C ARG* 5.8 0.2 - - - -
278C CYS* 3.4 35.4 - - - +
281C LEU* 3.7 29.2 - - + -
282C GLY 3.8 8.5 - - - +
285C TYR* 3.6 32.1 - + - -
293C LYS* 3.1 31.5 + - + +
294C ALA 4.0 0.7 - - - +
296C ASP* 1.3 83.6 - - - +
298C HIS* 1.3 65.2 + - - +
299C LEU 3.1 1.6 - - - -
300C LYS* 3.3 25.0 + - + +
301C HIS* 3.1 19.4 + - - +
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Residues in contact with HIS 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C TYR* 3.8 25.7 + + - -
282C GLY* 3.4 28.5 + - - -
283C ASN* 3.8 15.2 + - - -
286C THR* 4.3 5.9 + - - -
294C ALA* 2.9 31.2 + - + +
295C ILE* 4.7 0.9 - - - -
297C TYR* 1.3 76.6 - - - +
299C LEU* 1.3 58.2 + - - +
301C HIS* 3.5 5.7 + - - +
302C LEU* 3.0 27.2 + - - +
317C ALA* 4.5 3.4 + - - +
320C SER* 3.3 43.2 - - - -
321C LEU* 3.5 26.6 - - + +
324C ALA* 5.1 2.7 - - + -
28F VAL* 6.3 0.2 - - - +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ILE* 2.8 42.1 + - + +
296C ASP* 3.6 7.9 - - - +
298C HIS* 1.3 76.0 - - - +
300C LYS* 1.3 64.2 + - + +
302C LEU* 3.3 9.8 + - + +
303C ALA* 3.2 23.0 + - - +
321C LEU* 3.9 22.4 - - + -
325C TYR* 4.0 15.5 - - - +
337C PHE* 4.6 9.0 - - + -
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Residues in contact with LYS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ARG* 4.7 17.0 - - - +
278C CYS* 3.8 17.5 - - - -
296C ASP* 3.1 41.6 + - - +
297C TYR* 3.7 29.8 - - + +
299C LEU* 1.3 77.7 - - + +
301C HIS* 1.3 60.9 + - - +
303C ALA* 3.5 5.7 + - - +
304C ILE* 3.4 27.9 + - + +
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Residues in contact with HIS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA* 3.3 34.7 - - + +
276C GLN* 4.5 1.1 - - - -
278C CYS* 3.9 13.9 - - + +
279C TYR* 3.5 39.0 - + + +
297C TYR 3.1 16.4 + - - +
298C HIS* 3.8 5.1 + - - +
299C LEU 3.1 0.2 - - - -
300C LYS* 1.3 75.8 - - - +
302C LEU* 1.3 63.2 + - - +
304C ILE* 3.1 3.1 + - - +
305C ALA* 2.8 37.7 + - + +
310C ASP* 5.6 1.8 + - - -
313C GLY* 3.6 29.6 - - - -
316C ARG* 5.1 1.3 - - + -
317C ALA* 3.5 14.2 - - + +
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C HIS 3.0 18.1 + - - +
299C LEU* 3.3 9.8 + - + +
301C HIS* 1.3 80.5 + - - +
303C ALA* 1.3 57.2 + - - +
305C ALA* 3.3 2.3 + - - +
306C GLN* 2.9 65.9 + - + +
314C GLU* 4.2 17.9 - - + +
317C ALA* 3.9 18.6 - - + -
318C CYS* 4.6 5.8 - - - -
321C LEU* 3.9 9.4 - - + -
337C PHE* 3.7 32.1 - - + -
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ARG* 5.4 1.1 - - - +
299C LEU 3.2 10.2 + - - +
300C LYS* 3.7 10.8 - - - +
301C HIS 3.1 0.6 - - - -
302C LEU* 1.3 79.7 - - - +
304C ILE* 1.3 59.7 + - + +
306C GLN* 3.5 12.7 + - - +
307C GLU* 3.0 26.9 + - - +
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Residues in contact with ILE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ARG* 5.7 0.2 - - - +
271C ARG* 3.3 37.9 - - - +
274C GLU* 3.4 43.7 - - + +
275C ALA* 3.4 34.1 - - + +
278C CYS* 4.9 2.9 - - - -
300C LYS* 3.4 15.0 + - + +
301C HIS 3.1 3.6 + - - +
303C ALA* 1.3 75.6 - - + +
305C ALA* 1.3 60.5 + - - +
307C GLU* 3.0 7.8 + - - +
308C LEU* 2.9 44.5 + - + +
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA* 4.8 2.7 - - - +
301C HIS* 2.8 31.4 + - + +
302C LEU* 3.5 9.4 - - - +
304C ILE* 1.3 78.3 - - - +
306C GLN* 1.3 55.8 + - - +
308C LEU* 3.6 2.2 + - - -
309C ASN 3.1 5.2 + - - -
310C ASP* 2.7 44.9 + - + +
313C GLY* 4.3 1.6 - - - -
314C GLU* 4.1 25.4 - - + +
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Residues in contact with GLN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 2.9 51.0 + - + +
303C ALA* 3.7 12.8 - - - +
305C ALA* 1.3 75.9 - - - +
307C GLU* 1.3 66.6 + - - +
309C ASN* 2.9 14.4 + - - +
314C GLU* 3.4 33.2 + - - +
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Residues in contact with GLU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ARG* 3.0 43.3 + - - +
303C ALA 3.0 15.2 + - - +
304C ILE* 3.3 8.6 - - - +
306C GLN* 1.3 78.8 - - - +
308C LEU* 1.3 73.5 + - + +
309C ASN* 3.3 3.8 + - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ARG* 4.1 10.3 - - + -
272C ALA* 3.9 30.5 - - + +
275C ALA* 5.4 1.3 - - + -
304C ILE* 2.9 36.3 + - + +
305C ALA* 4.2 3.6 - - - +
307C GLU* 1.3 91.6 - - + +
309C ASN* 1.3 69.9 + - - +
310C ASP* 3.0 9.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il